During the first years of the Baltic Assembly's activities the need for closer links between the Baltic Assembly and the governments of the Baltic States arose.

On 26 January 1992, the Baltic Assembly adopted the Final Document of the First Plenary Meeting by inviting the governments of the Baltic States to prepare interstate agreement with aim of creating a legal basis for mutual cooperation. On 31 October 1993 in Tallinn, the Baltic Assembly adopted Resolution on the Baltic Council by asking the governments of the Baltic States "to draft, as soon as possible a respective tripartite agreement providing for the formation of the Council of Ministers of the Baltic States and its budget." On 25 April 1994, the governments of the Baltic States agreed about the draft Agreement on Baltic cooperation and cooperation formats between the Baltic Assembly and the Baltic Council of Ministers. On 15 May 1994, the Baltic Assembly adopted Resolution concerning the Draft Agreement on Baltic Cooperation between the Republic of Estonia, the Republic of Latvia and the Republic of Lithuania by recommending to sign this Agreement as soon as possible.

On 13 June 1994 in Tallinn, Agreement on Baltic Parliamentary and Governmental Cooperation between the Republic of Estonia, the Republic of Latvia and the Republic of Lithuania was signed. The Agreement defined the responsibilities of the Baltic Assembly and the Baltic Council of Ministers; and designated the Baltic Council as the main forum of both organizations.

As of 2003 the same country holds the presidency in both organizations for one year, thus enabling the Baltic Assembly and the Baltic Council of Ministers to identify common priorities and tasks more efficiently and to coordinate the work of their organizational units more successfully. In accordance with the Protocol Amending the Protocol on Cooperation between the Baltic Assembly and the Baltic Council of Ministers, adopted by the 10th Baltic Council on 18 December 2004, the key cooperation forms between both organizations are the following:

Annual meetings of the Baltic Assembly and the Baltic Council of Ministers are held during the Baltic Council

Joint meetings of the BA Presidium and the Cooperation Council of the BCM, which is composed of foreign affairs ministers

Report of the Chairman of the Cooperation Council of the BCM about the work accomplished during the year of presidency

Answers to the questions submitted by the members of the Baltic Assembly provided by the Chairman of the Cooperation Council of the BCM

Cooperation among committees and secretariats of both organisations

Cooperation between the Baltic Assembly and the Baltic Council of Ministers in 2019

In 2019, Latvia was holding presidency in the Baltic Assembly and the Baltic Council of Ministers. Parliamentary and governmental cooperation focused on three main priorities:

Strengthening security in the region;

Developing regional connectivity with a focus on energy and transport infrastructure and digital agenda;

Promoting common interests within the EU.

On 29 November 2019 in Riga, the Baltic Assembly and the Baltic Council of Ministers convened for the 25th Baltic Council to discuss cooperation in security and defence, to review progress in developing regional energy and transport infrastructure projects and to discuss common position of the Baltic States on the 2021-2027 EU Multiannual Financial Framework and to define objectives of Baltic parliamentary and governmental cooperation in 2020. President of the Baltic Assembly and Chairman of the Cooperation Council of the Baltic Council of Ministers signed Joint Statement of the 25th Baltic Council.

Cooperation between the Baltic Assembly and the Baltic Council of Ministers in 2020

In 2020, Estonia is holding the presidency in the Baltic Assembly and the Baltic Council of Ministers.

The Baltic Assembly and the Baltic Council of Ministersjoint priorities for cooperation in 2020:

Protocol amending the Agreement on Baltic Parliamentary and Governmental Co-operation between the Republic of Estonia, the Republic of Latvia and the Republic of Lithuania on 28 November 2003 in Vilnius, Lithuania